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Merge pull request #1404 from virtualcell/repair-nightly-testing
Fixed BMDB Nightly testing, and upgrade with better logging
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83 changes: 83 additions & 0 deletions
83
vcell-cli/src/main/java/org/vcell/cli/testing/TestReportCommand.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,83 @@ | ||
| package org.vcell.cli.testing; | ||
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| import org.apache.logging.log4j.Level; | ||
| import org.apache.logging.log4j.LogManager; | ||
| import org.apache.logging.log4j.Logger; | ||
| import org.apache.logging.log4j.core.LoggerContext; | ||
| import org.vcell.sedml.testsupport.OmexExecSummary; | ||
| import org.vcell.sedml.testsupport.OmexTestCase; | ||
| import org.vcell.sedml.testsupport.OmexTestReport; | ||
| import org.vcell.sedml.testsupport.OmexTestingDatabase; | ||
| import picocli.CommandLine.Command; | ||
| import picocli.CommandLine.Option; | ||
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| import java.io.File; | ||
| import java.nio.file.Files; | ||
| import java.util.List; | ||
| import java.util.concurrent.Callable; | ||
| import java.util.function.Predicate; | ||
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| @Command(name = "test-report", description = "create test reports for a test suite") | ||
| public class TestReportCommand implements Callable<Integer> { | ||
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| private final static Logger logger = LogManager.getLogger(TestReportCommand.class); | ||
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| @Option(names = { "-t", "--test-cases" }, required = false, description = "[optional] test cases file - defaults to embedded test cases") | ||
| private File testCasesNdjsonFile; | ||
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| @Option(names = { "-e", "--exec-summaries" }, required = true, description = "test results file e.g. exec_summary.ndjson") | ||
| private File execSummaryNdjsonFile; | ||
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| // list of OmexTestingDatabase.TestCollection objects to include | ||
| @Option(names = { "-c", "--collections" }, required = true, description = "list of test collections to include") | ||
| private List<OmexTestingDatabase.TestCollection> collections; | ||
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| @Option(names = { "--report-md" }, required = true, description = "filename for generated markdown test report (e.g. ./report.md)") | ||
| private File reportFile_md; | ||
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| @Option(names = { "--report-json" }, required = false, description = "filename for generated json test report (e.g. ./report.json)") | ||
| private File reportFile_json; | ||
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| @Option(names = { "-d", "--debug" }, description = "enable debug logging") | ||
| private boolean bDebug = false; | ||
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| public Integer call() { | ||
| Level logLevel = bDebug ? Level.DEBUG : logger.getLevel(); | ||
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| LoggerContext config = (LoggerContext)(LogManager.getContext(false)); | ||
| config.getConfiguration().getLoggerConfig(LogManager.getLogger("org.vcell").getName()).setLevel(logLevel); | ||
| config.getConfiguration().getLoggerConfig(LogManager.getLogger("cbit").getName()).setLevel(logLevel); | ||
| config.updateLoggers(); | ||
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| try { | ||
| // read test cases and filter by collections | ||
| Predicate<OmexTestCase> omexTestCasePredicate = tc -> collections.contains(tc.test_collection); | ||
| final List<OmexTestCase> testCaseList; | ||
| if (testCasesNdjsonFile != null) { | ||
| String test_cases_contents = Files.readString(testCasesNdjsonFile.toPath()); | ||
| testCaseList = OmexTestingDatabase.parseOmexTestCases(test_cases_contents).stream().filter(omexTestCasePredicate).toList(); | ||
| } else { | ||
| // if file not specified, use embedded test cases | ||
| testCaseList = OmexTestingDatabase.loadOmexTestCases().stream().filter(omexTestCasePredicate).toList(); | ||
| } | ||
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| // read exec summaries | ||
| String exec_summary_contents = Files.readString(execSummaryNdjsonFile.toPath()); | ||
| List<OmexExecSummary> execSummaries = OmexTestingDatabase.loadOmexExecSummaries(exec_summary_contents); | ||
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| // generate report | ||
| OmexTestReport report = OmexTestingDatabase.generateReport(testCaseList, execSummaries); | ||
| if (reportFile_json != null) { | ||
| Files.writeString(reportFile_json.toPath(), report.toJson()); | ||
| } | ||
| if (reportFile_md != null) { | ||
| Files.writeString(reportFile_md.toPath(), report.toMarkdown()); | ||
| } | ||
| return 0; | ||
| } catch (Exception e) { | ||
| throw new RuntimeException(e.getMessage(), e); | ||
| } finally { | ||
| logger.debug("Completed all exports"); | ||
| } | ||
| } | ||
| } |
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